In the quest for new lead generation strategies, biophysical approaches are being relied upon more heavily in drug discovery, especially for drug targets that have been traditionally harder to study such as protein-protein interactions (PPIs) and membrane proteins. Biophysical tools, which are based on measuring interactions between two biological molecules, have advanced in their automation so that they now enable screening of protein complexes, PPIs and fragment-based drug leads, where there is no enzymatic readout around which to build a biochemical high throughput assay. Many biophysical techniques also allow targets to be analyzed in their native environment, a bonus for working with difficult-to-isolate membrane proteins. Join fellow structural, biophysical, computational and discovery chemists and biologists for this one-day symposium where different biochemical techniques will be introduced and covered via case studies on an application level. Discussions will also center on when and how to use which method and integration of various approaches – beneficial to the medicinal chemist who has to choose which technique to use depending on the project’s needs.

Final Agenda

Thursday, April 27

7:25 am Registration and Morning Coffee

INTEGRATING BIOPHYSICAL APPROACHES

7:55 Chairperson’s Opening Remarks

Derek Cole, Ph.D., Director, Medicinal Chemistry, Takeda

8:00 FEATURED PRESENTATION: Combining Biophysical Techniques for Difficult Targets: Case Vignettes

Jonathan Blevitt, Ph.D., Principal Scientist, Discovery Sciences, Janssen R&D

 

8:30 Applications of the Thermal Shift Assay: More than Melts the Eye

Mary Harner, Ph.D., Research Investigator II, Leads Discovery & Optimization, Bristol-Myers Squibb

The thermal shift assay (TSA) is a commonly employed biophysical method for characterization of molecular properties and molecular interactions. However, TSA has taken a back seat to novel and rising biophysical technologies that are deemed more information-rich than a simple protein melting curve. This talk will highlight applications of TSA including fragment screening, SAR support orthogonal to biochemical assay formats, X-ray crystallography surrogate identification, binding selectivity panels, binding mechanism, target destabilization, and metal contamination studies.

9:00 Coffee Break

9:30 Kinetic and Thermodynamic Profiling in Drug Discovery: Are We There Yet?

Ying Wang, Ph.D., Principal Research Scientist, Department of Chemistry and Technology, AbbVie

Extensive kinetic and thermodynamic data were collected and analyzed via SPR and ITC throughout the hit to tool/lead and high throughput screening campaigns for the identification of allosteric inhibitor of the PRC2 complex through EED binding. Correlations with biochemical data and structural information will be presented as well as our perspectives on where we are at on harnessing the power of thermodynamic and kinetic profiling in drug discovery.

10:00 Combining X-Ray Crystallography, SPR and ITC to Understand the Structure-Binding Kinetic Relationships of a Type I CDK Inhibitor

Pelin Ayaz, Ph.D., Postdoctoral Researcher, Chemistry, Biology, and Drug Discovery, D.E. Shaw Research

Roniciclib is a type I pan-CDK (cyclin dependent kinase) inhibitor that displays prolonged residence times on CDK2 and CDK9, whereas residence times on other CDKs are transient, thus giving rise to a kinetic selectivity of Roniciclib. This work is one of the few known examples of an SKR (structure – binding kinetics relationships) study in a pharma development pipeline.

10:30 Affinity Selection Mass Spectrometry for Target Validation and Hit Triage

Jeff Messer, Director, NCE Molecular Discovery, GSK

Biophysics in Hit ID is deployed to screen and/or qualify hits from biochemical screens. GSK’s Encoded Library Technology selects small molecule binders from large combinatorial mixtures (>1E9) then deconvolutes structure by DNA barcode. We will share semi-quantitative methods that we have developed to qualify primary hits from combinatorial mixture or crude compound re-prep that uses DNA or mass encoding respectively.

11:00Enjoy Lunch on Your Own

SPECIFIC BIOPHYSICAL TECHNIQUES

1:00 pm Chairperson’s Remarks

Chris Smith, Ph.D., Director, Medicinal Chemistry, COI Pharmaceuticals

1:05Nanoscale Encapsulation for Optimized Fragment Based Drug Discovery

Joshua Wand, Ph.D., Professor, Biochemistry & Biophysics, University of Pennsylvania

Weak binding is an unfortunate hallmark of "hits" derived from fragment based libraries. This often requires direct demonstration of a physical interaction prior to elaboration and functional testing. Utilizing the reverse micelle as a confined space, we show that solution NMR spectroscopy can be used to efficiently detect weak specific binding; reduce or eliminate non-specific binding; significantly reduce the amount of ligand and protein required; and, most importantly, enter a region of chemical space that is highly desired but difficult to access using existing screening strategies (i.e. weak hydrophilic binders).

1:35 Interpreting Fragment-Target X-Ray Crystals

Anthony Bradley, Ph.D., Postdoctoral Researcher, Diamond Light Source and Department of Chemistry, University of Oxford

X-Chem is a union of high-throughput X-Ray screening, analysis tools and chemistry to enable rapid fragment-based chemical probe development. Making use of bespoke tools, we are able to develop and analyse 1,000s of datasets in a semi-automated manner and determine the binding modes of weakly bound fragments. From this, in-house analysis tools aid chemists to make informed decisions regarding which compounds to design next.

2:05 Cryo-EM as a Tool for Discovery and Development of Viral Vaccines

Erin Tran, Ph.D., Staff Scientist, Laboratory of Cell Biology, Biophysics Section, National Cancer Institute, Center for Cancer Research, National Institutes of Health

Using cryo-electron tomography, viral surface proteins can be visualized in three dimensions in a near-native state. We used tomographic subvolume averaging to structurally characterize the surface glycoproteins of HIV, influenza and Ebola. By analyzing membrane-bound viral glycoprotein structures in the presence or absence of cellular receptors or neutralizing antibodies, we are gaining insights into the dynamic range of glycoprotein conformational states as well as potential mechanisms of antibody-based vaccine neutralization.

2:35 Refreshment Break

BIOPHYSICAL APPROACHES FOR MEMBRANE PROTEINS

3:05 Fragments and SPR for GPCRs

Shuo Wang, Ph.D., Staff Scientist, Structural Biology and Biophysics, Takeda California

As a label free, real-time and high throughput methodology, SPR is one of the most powerful biophysical approaches for fragment library screening. An advanced application is fragment screening using SPR on membrane protein targets, such as GPCRs. This talk focuses on the technical aspects of fragment screening by SPR on solubilized wild type receptors.

3:35 A Bio-Electronic Sensor for Cell-Free, Label-Free Study of GPCR-Ligand Interactions on Native Cell Membranes

Jaime Arenas, Ph.D., Director, Assay Development, Sensor Technology, Nanotech Biomachines, Inc.

The ability to characterize the kinetic binding of drug candidates to native GPCR and other integral membrane protein targets is a critical unmet need in the lead generation process for these targets. I will discuss capabilities of our graphene-based electronic sensor for cell-free and label-free measurement of kinetic binding to integral membrane protein targets in their native conformation in grafted cell membranes.

4:05 M2 Proton Channel of Influenza Studied by NMR Spectroscopy

Yibing Wu, Ph.D., Specialist, Department of Pharmaceutical Chemistry, University of California, San Francisco

The M2 protein is a highly proton selective channel that is essential for the virus life cycle. We used solution NMR to investigate the channel opening/closing and drug inhibition mechanisms. This structure is the first high-resolution M2 mutant structure and will aid our structure-guided drug development efforts.

4:35 Close of Symposium

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